If your LCA's are stock then they told you wrong, whether fronts or rears. Toe shouldn't be affected by lowering. It's camber. Some shops are asses and won't align a lowered car. What I'd do is call around and find one that will do an alignment. Usually they will just give you a disclaimer about aligning your car as close to factory specs as possible.
If more than 1.75 inch drop, it would be in your best interest to install front and rear camber kits.
Good luck.